merge_PCR_tool.xml

<tool id="chromosome_info_pysam.py" name="Merge duplicates" version="0.1.0">
  <description>according to random barcode library.</description>
  <version_command>python $__tool_directory__/chromosome_info_pysam.py </version_command>
  <requirements>
    <requirement type="package">Biopython</requirement>
    <requirement type="package" version="0.11.1">pysam</requirement>
    <requirement type="package">argparse</requirement>

  </requirements>
  <!-- interpreter attribute is deprecated and $__tool_directory__ variable is superior -->
  <command interpreter="python"><![CDATA[chromosome_info_pysam.py
$bam_file
$fastaq_file
#if $Sequnce_end and $Sequnce_end is not None:
$Sequnce_end
#end if
#if $XS_tag and $XS_tag is not None:
$XS_tag
#end if
--output_file $out_file]]></command>
  <inputs>
    <param area="false" label="bam file." name="bam_file" type="data" format="bam"/>
    <param area="false" label="fastaq barcode library." name="fastaq_file" type="data" format="fastq"/>
    <!--param area="false" value="True" label="End of File." argument= "-e" name="e" type="boolean" optional="true"/-->
   <param type="boolean" truevalue="-t" falsevalue="" name="XS_tag"/> 
   <param type="boolean" truevalue="-e" falsevalue="" name="Sequnce_end"/>
  </inputs>
  <outputs>
    <data format="bed" hidden="false" name="out_file"/>
  </outputs>
  <tests>
    <test>
      <param name="bam_file" value="example3_inputa.bam"/>
      <param name="fastaq_file" value="example3_inputb.fastq"/>
      <param name="o" value="result.bed"/>
      <param name="XS_tag" value="True"/>
      <param name="Sequnce_end" value="True"/>
      <output name="out_file" file="Output_Result.bed"/>
    </test>
  </tests>
  
</tool>